Visualize HRR analysis results

You can visualize data that is relevant to Homologous Recombination Repair (HRR) in Ion Reporter™ Software, with the Oncomine™ Comprehensive Assay Plus panel.

HRR is a pathway to repair double-strand breaks which are generated as by-products of cellular metabolism, DNA replication errors, or exogenous factors. The biomarkers that are associated with HRR can indicate alterations in genes and genomes. An HRR visualization shows details about the genomic loss-of-heterozygosity in the sample (%LOH). Additionally, information about Telomeric Allelic Imbalance (%TAI) and Large-Scale State Transitions (%LST) biomarkers is available in the VCF file that you can download when you open HRR analysis results.

  1. Do one of the following to open HRR analysis results:

    Option

    Description

    Visualize analysis results from an individual sample or from multiple samples simultaneously from the Analyses table.

    In the Analyses table, select an individual sample result row, or select the checkbox next to each sample result that you want to visualize simultaneously, then click Visualize. Alternatively, click Actions > Visualize.

    Visualize analysis results individually from the Analysis Results screen.

    In the Analyses table, click a sample result hyperlink in the Analysis column to open the Analysis Results, then click Visualize.

    The Analysis Visualization opens to the TMB tab by default.

  2. Select the HRR tab to review a summary of the analysis results about the genes and genomic alterations in the HRR pathway. For example, you can view information about genomic LOH (sample %LOH), CNVs, SNVs, and INDELs. You can also view any exon-level deletions and duplications that are associated with BRCA1 and BRCA2 genes.
  3. Click Download > Current Results TSV to download a tab-separated list of detected variants in the analysis results. Open the file with compatible software, such as Microsoft™ Excel™.

    For more information on the download files, see Download filtered variants.

  4. Click Download > Filtered Variants or Download > All Variants to download a ZIP folder of files that list the variants in the analysis results.

    The file hrr_summary.tsv is included in the downloaded results.

  5. Select the BRCA tab to visualize information about whole exon and multiple exon deletion in the BRCA1 and BRCA2 genes in somatic and germline samples with high sensitivity. For more information, see View Oncomine BRCA analysis results.
  6. Select the IRGV & Generate Report tab, then click Generate Report to create and download a visualization report in PDF format, which includes the analysis results with graphs and metrics. For more information, see Create a visualization report
Related Topics
Parent topic: Visualize analysis results with Ion Reporter™ Software